A federal agency said it found serious track defects on several important routes operated by CSX Corp., as well as a lack of quality control in the company's track-maintenance and inspection programs.

The Federal Railroad Administration said that in a two-week investigation between Feb. 22 and March 3 of about 4,000 miles of track, it found the defects, including some spots where the rails had spread too far apart, a problem that could cause a train to derail. Some of the areas that showed the most track wear carry a large...